We previously reported that immunization with recombinant SIVmne envelope (gp160) vaccines protected macaques against intravenous challenge by the cloned homologous virus, E11S, but protection was only partially effective against the uncloned virus, SIVmne. In the present study, we examined the protective efficacy of this immunization regimen against infection by a mucosal route. We found that the same gp160-based vaccines were highly effective against intrarectal infection not only by the E11S clone but also by the uncloned SIVmne. Protection against mucosal infection is therefore achievable by parenteral immunization with recombinant envelope vaccines. Protection appears to correlate with the presence of serum-neutralizing activities and high levels of SIV-specific antibodies. To understand the basis for the differential efficacy against the uncloned virus by the intravenous versus the intrarectal routes, we examined viral sequences recovered from the PBMC of anim als early after infection by both routes. We previously showed that 85% of the uncloned SIVmne challenge stock contained V1 sequences homologous to the molecular clone from which the vaccines were made (E11S type); the remainder (15%) contained multiple conserved changes (the variant types). In contrast to intravenously infected animals, from which either E11S-type or the variant type V1 sequences could be recovered in significant proportions, animals infected intrarectally had predominantly E11S-type sequences. Preferential transmission or amplification of the E11S-type viruses may therefore account in part for the enhanced efficacy of the recombinant gp160 vaccines against the uncloned virus challenge by the intrarectal route as compared with the intravenous route. Seven animals are being held for rechallenge studies. FUNDING NIH grant RR00166. Polacino, P., V. Stallard, D. C. Montefiori, C. R. Brown, B. A. Richardson, W. R. Morton, R. E. Benveniste, and S.-L. Hu. Protection of macaques against intrarectal infection by a combination immunization regimen with recombinant SIVmne gp160 vaccines. J. Virol. 73:3134-3146, 1999.